[ensembl-dev] Dev Digest, Vol 23, Issue 1

Kurt Hetrick khetric1 at jhmi.edu
Mon Jan 4 18:44:39 GMT 2021

Thanks Andrew,

The part that led me to believe that using hgvs in offline mode was possible was in the vep options page, but maybe I was misreading them...based on your answer, using it for when the input is hgvs is not possible, but it might be possible for when you want to annotate a file with hgvs and your input is not hgvs (which I also will want to do)...which I haven't attempted yet, but plan to do so in the near future.


for the --fasta and --hgvs flags.

--fasta [file|dir]

Specify a FASTA file or a directory containing FASTA files to use to look up reference sequence. The first time you run VEP with this parameter an index will be built which can take a few minutes. This is required if fetching HGVS annotations (--hgvs<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_hgvs>) ...


Add HGVS<https://varnomen.hgvs.org/> nomenclature based on Ensembl stable identifiers to the output. Both coding and protein sequence names are added where appropriate. To generate HGVS identifiers when using --cache<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache> or --offline<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_offline> you must use a FASTA file and --fasta<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fasta>. HGVS notations given on Ensembl identifiers are versioned<https://m.ensembl.org/info/genome/stable_ids/index.html>. Not used by default


Add genomic HGVS<https://varnomen.hgvs.org/> nomenclature based on the input chromosome name. To generate HGVS identifiers when using --cache<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache> or --offline<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_offline> you must use a FASTA file and --fasta<https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fasta>. Not used by default

There are other parts of the online documentation that stated that it was not possible for various reasons, but the above is what led me to believe that it might be possible.

Best Regards,

Kurt Hetrick

Message: 2

Date: Mon, 4 Jan 2021 18:22:50 +0000

From: Andrew Parton <aparton at ebi.ac.uk<mailto:aparton at ebi.ac.uk>>

To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>

Subject: Re: [ensembl-dev] hgvs in offline mode.

Message-ID: <DF835DE9-2062-4EB4-81AA-84798B69AA10 at ebi.ac.uk<mailto:DF835DE9-2062-4EB4-81AA-84798B69AA10 at ebi.ac.uk>>

Content-Type: text/plain; charset="utf-8"

Hi Kurt,

Unfortunately the error is correct, you cannot use HGVS input format in offline mode.

If there?s something incorrect or unclear in our docs then I would like to update it, could you please point in the direction of the documentation you found?

Kind Regards,


> On 4 Jan 2021, at 17:54, Kurt Hetrick <khetric1 at jhmi.edu<mailto:khetric1 at jhmi.edu>> wrote:


> Hello,


> From reading the online documentation I was under the impression that one could use hgvs in offline mode provided that they pointed to the fasta file, but the error I received suggests otherwise. Am I missing something or is hgvs not possible in offline mode. Using GRCh37.


> I am using a singularity image for ensemble 102 that I pulled from a docker image that I built using the dockerfile from your dockerhub page where I changed the base image from Ubuntu 18.04 to Ubuntu 16.04 and then built the cache locally.


> export PERL5LIB=/mnt/resources/vep_data export

> PATH=$PATH:/mnt/resources/vep_data


> singularity exec -B /mnt:/mnt /mnt/containers/vep-102.0.simg vep -i

> file2.txt -o test.vcf --fork 4 --cache --offline --refseq

> --force_overwrite --dir /mnt/resources/vep_data --fasta

> /mnt/research/tools/test/human_g1k_v37_decoy.fasta --hgvs --assembly

> GRCh37 --check_existing --dir_cache /mnt/resources/vep_data

> 2021-01-04 17:43:09 - INFO: BAM-edited cache detected, enabling

> --use_transcript_ref; use --use_given_ref to override this


> -------------------- EXCEPTION --------------------

> MSG: ERROR: Cannot use HGVS format in offline mode STACK

> Bio::EnsEMBL::VEP::Parser::HGVS::new

> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm:104

> STACK Bio::EnsEMBL::VEP::Parser::new

> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:151

> STACK Bio::EnsEMBL::VEP::Runner::get_Parser

> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:805

> STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer

> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:832

> STACK Bio::EnsEMBL::VEP::Runner::init

> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:140

> STACK Bio::EnsEMBL::VEP::Runner::run

> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203

> STACK toplevel /opt/vep/src/ensembl-vep/vep:229

> Date (localtime)    = Mon Jan  4 17:43:09 2021

> Ensembl API version = 102


> head -n 5 file2.txt

> NM_000492.4:c.-13_10del23

> NM_000492.4:c.-9_14del23

> NM_000492.4:c.-8G>C

> NM_000492.4:c.[1046C>T;3747delG]

> NM_000492.4:c.[1093_1094delCT;3705T>G]


> Thanks in advance,


> Kurt Hetrick


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